wrap-up

This is not a standalone tool or extension. It's a project template containing context files, slash commands, and configuration that guide VS Code's GitHub Copilot to behave as a specialized research assistant.

Clone this template for each new research project. The RA will:

• Guide you through research phases (planning → development → analysis → writing)
• Help write manuscript sections from your actual code and data
• Ensure reproducibility through proper documentation and DVC pipelines
• Track tasks and action items from meetings
• Conduct regular reviews to keep you on track

```bash

# Clone the template

git clone https://github.com/[username]/research-assistant-template my-new-project

cd my-new-project

# Remove template's git history

rm -rf .git

git init

# Open in VS Code

code .

```

Then open GitHub Copilot Chat and type:

```

/next

```

The RA will guide you through setup.

"Feed the Beast" - The RA is only as good as the context you give it.

This template provides:

• Context files that tell the RA about your project and preferences
• Slash commands that define specific workflows
• Templates for manuscript sections, figure captions, and reviews
• Phase gates that prevent skipping critical reproducibility steps

🎯 Phase-Based Guidance

Projects progress through: SETUP → PLANNING → DEVELOPMENT → ANALYSIS → WRITING → REVIEW

The RA tracks where you are and won't let you skip critical steps.

📝 Manuscript Integration

Write your methods section as you code. Generate results from figures. Draft background from literature reviews.

🔍 Literature Research

Deep research with verified citations. No hallucinated references.

📋 Task Management

Extract action items from meeting transcripts. Route to tasks.md or GitHub Issues based on complexity.

📊 Regular Reviews

Weekly project check-ins. Monthly alignment checks. Quarterly mission reviews.

| Command | Purpose |

|---------|---------|

| /next | Start here. Get suggested next steps based on project state. |

| /deep_research [topic] | Literature search with verified citations |

| /write_background | Draft background section from literature |

| /write_methods | Generate methods from documented scripts |

| /write_results | Draft results from figures and captions |

| /review_script [path] | Check code documentation quality |

| /weekly_review | Weekly progress review |

| /monthly_review | Monthly alignment check |

| /quarterly_review | Quarterly mission review |

| /plan_week | Create focused weekly plan |

| /transcribe [file] | Transcribe meeting audio |

| /summarize_meeting [file] | Extract action items from transcript |

```

├── .ra/ # RA tool framework

│ ├── copilot-instructions.md # RA brain and personality

│ ├── commands/ # Slash command definitions

│ └── tools/ # RA utilities (transcribe.py, etc.)

├── .research/

│ ├── project_telos.md # Your project's aims and state

│ ├── phase_checklist.md # Progress tracking

│ ├── literature/ # Research outputs with citations

│ ├── meetings/ # Meeting recordings and transcripts

│ │ ├── audio/ # Audio files (.m4a, .mp3, .wav)

│ │ └── transcripts/ # Transcript markdown files

│ └── logs/ # Activity and review logs

├── data/

│ ├── raw/ # Immutable source data

│ ├── processed/ # Derived data

│ └── .sensitive/ # Excluded from AI (IRB data, etc.)

├── scripts/ # Your analy